The value of different staining methods for rapid analysis of transbronchial needle aspirates during bronchoscopy has not been explored. In the present study, we compared a Papanicolaou-based rapid stain, prepared by a technologist and read by a cytopathologist, and a Wright-Giemsa-based rapid stain, prepared and read by a cytopathologist alone. Gold standard was the final laboratory report issued on each aspirate. We harvested 827 aspirates from 218 target sites in 126 consecutive patients. At least one positive aspirate was found in 99 (79%) patients. In those 99 patients, 288 of 574 (50%) aspirates were positive for neoplastic (83%) or non-neoplastic (17%) disease. False-negative aspirates and target sites were more frequent with the rapid Wright-Giemsa than with the rapid Papanicolaou stain (14.2 versus 7.3%, p = 0.008, and 13.7 versus 3.6%, p = 0.021, respectively). The sensitivity of the Wright-Giemsa-based and Papanicolaou-based rapid stains for detecting diagnostic material was 93 and 100% in patients, 83.1 and 95.5% in target sites, and 72.8 and 84.9% in aspirates, respectively. Specificity was 100% for both methods in patients and target sites, and 90.4 and 95% in aspirates. We concluded that a Papanicolaou-based stain has superior yield and accuracy to a Wright-Giemsa-based stain for rapid on-site evaluation of transbronchial needle aspirates.